In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.

https://escholarship.org/content/qt87m969xt/qt87m969xt.pdf?t=q8vzhb

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.

International Network of Cancer Genome Projects

Genomic sequencing is rapidly transitioning into clinical practice, and implementation into healthcare systems has been supported by substantial government investment, totaling over US$4 billion, in at least 14 countries. These national genomic-medicine initiatives are driving transformative change under real-life conditions while simultaneously addressing barriers to implementation and gathering evidence for wider adoption. We review the diversity of approaches and current progress made by national genomic-medicine initiatives in the UK, France, Australia, and US and provide a roadmap for sharing strategies, standards, and data internationally to accelerate implementation.

/pdf/integrating-genomics-into-healthcare-a-global-responsibility-4z7col3gfb.pdf

Integrating Genomics into Healthcare: A Global Responsibility

A fundamental problem in rare-disease diagnostics is the lack of consensus as to which genes have sufficient evidence to attribute causation. To address this issue, we have created PanelApp (
 https://panelapp.genomicsengland.co.uk
 ), a publicly available knowledge base of curated virtual gene panels.

PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels.

Personalized Medicine and the Power of Electronic Health Records.

In partnership with NHS England, Genomics England’s ambitious plans to embed genomic medicine into routine patient care are well underway. Clare Turnbull and colleagues discuss its progress

/pdf/the-100-000-genomes-project-bringing-whole-genome-sequencing-1ci2ge2xil.pdf

Lisa Dinh

Papers

The 100 000 Genomes Project: bringing whole genome sequencing to the NHS